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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-107644804-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=107644804&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 107644804,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_005443.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Glu502Lys",
"transcript": "NM_005443.5",
"protein_id": "NP_005434.4",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 624,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265174.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005443.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Glu502Lys",
"transcript": "ENST00000265174.5",
"protein_id": "ENSP00000265174.4",
"transcript_support_level": 1,
"aa_start": 502,
"aa_end": null,
"aa_length": 624,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005443.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265174.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1573G>A",
"hgvs_p": "p.Glu525Lys",
"transcript": "ENST00000873396.1",
"protein_id": "ENSP00000543455.1",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 647,
"cds_start": 1573,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873396.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Glu501Lys",
"transcript": "ENST00000970503.1",
"protein_id": "ENSP00000640562.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 623,
"cds_start": 1501,
"cds_end": null,
"cds_length": 1872,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970503.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Glu502Lys",
"transcript": "ENST00000931561.1",
"protein_id": "ENSP00000601620.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 622,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931561.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1495G>A",
"hgvs_p": "p.Glu499Lys",
"transcript": "ENST00000931560.1",
"protein_id": "ENSP00000601619.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 621,
"cds_start": 1495,
"cds_end": null,
"cds_length": 1866,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931560.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1492G>A",
"hgvs_p": "p.Glu498Lys",
"transcript": "ENST00000970505.1",
"protein_id": "ENSP00000640564.1",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 620,
"cds_start": 1492,
"cds_end": null,
"cds_length": 1863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970505.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1450G>A",
"hgvs_p": "p.Glu484Lys",
"transcript": "ENST00000970504.1",
"protein_id": "ENSP00000640563.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 606,
"cds_start": 1450,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970504.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Glu351Lys",
"transcript": "ENST00000931559.1",
"protein_id": "ENSP00000601618.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 473,
"cds_start": 1051,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931559.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.871G>A",
"hgvs_p": "p.Glu291Lys",
"transcript": "ENST00000931563.1",
"protein_id": "ENSP00000601622.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 413,
"cds_start": 871,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931563.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1441G>A",
"hgvs_p": "p.Glu481Lys",
"transcript": "XM_011532400.3",
"protein_id": "XP_011530702.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 603,
"cds_start": 1441,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532400.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.1441G>A",
"hgvs_p": "p.Glu481Lys",
"transcript": "XM_011532401.2",
"protein_id": "XP_011530703.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 603,
"cds_start": 1441,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532401.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"hgvs_c": "c.670-12944G>A",
"hgvs_p": null,
"transcript": "ENST00000931562.1",
"protein_id": "ENSP00000601621.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 345,
"cds_start": null,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931562.1"
}
],
"gene_symbol": "PAPSS1",
"gene_hgnc_id": 8603,
"dbsnp": "rs749060064",
"frequency_reference_population": 0.0000041201206,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000412012,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9264109134674072,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.734000027179718,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.622,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9986,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.428,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.906370276182654,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005443.5",
"gene_symbol": "PAPSS1",
"hgnc_id": 8603,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Glu502Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}